[MMTK] dcd_to_nc : IOError: Database entry Atoms/ not found

Jaroslaw Kalinowski jak at biogeo.uw.edu.pl
Fri Aug 1 08:29:29 UTC 2008


 Hi,

Seems that your problem is not dcd-related.
You have:

>>   File "/usr/bin/dcd_to_nc", line 110, in <module>
>>     universe.addObject(conf.createAll())

And the important fragments fom dcd_to_nc script are:

   16 usage = """Usage: dcd_to_nc [options] pdb_file dcd_file nc_file
   17
   18 pdb_file and dcd_file must describe the same system.

  109 conf = PDBConfiguration(pdb_file)
  110 universe.addObject(conf.createAll())

It means that the problem occurs while reading pdb file.
You also have:

>>     raise IOError("Database entry %s/%s not found" % (directory,
>> filename))
>> IOError: Database entry Atoms/  not found

Which means that for some reason it is looking for an atom that has space
(' ') as a symbol, which obviously it can not find.

Check your pdb file. Make sure it has well formatted atom names in correct
columns. Please note that atom field is 4 characters long and must have
spaces in right place. For example you should have ' C  ' or  and not '  
C' or '  C ' or 'C   '. See Notes on atom naming in
http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html

Best wishes,

JAK



More information about the mmtk mailing list